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The base packages ship pretty generic code, which means most packages aren't going to take advantage of the Cuda support on the TK1. Even getting Nvidia's optimized version of OpenCV to work with ROS can be a bit challenging.
Neither board will run Rviz well. (The TK1 can run Rviz, but I don't recommend it)
The CPU cores in the TK1 are very roughly on par with the Pi3 (I haven't run thorough comparison benchmarks)
The Pi3 has a fully removable disk (SD card), so flashing it, recovering it, and making backups is a lot easier than the TK1, which uses non-removable storage.
The Pi3 has more USB ports and the GPIO probably has better support.
The TK1 has CUDA, a USB3 port and mini-PCIe slot.
In general, I'd recommend that you get the Pi3 unless you really need the features that are available on the TK1.
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